Wheat (Triticum aestivum L.), the staple foot for one third of the world population, is one of the three most important crop plants worldwide. In 2014, 730 M t of wheat seeds were produced on an area of 220 M ha, with a global average yield of 3.6 t/ha. To meet the projected demand of 70 % more food by the middle of this century, wheat yields must be almost doubled within the next few decades. However, trends indicate current stagnation of yield levels in the major wheat growing regions of Europe, North America, Asia and Australia. This is mainly attributed to a narrow genetic diversity in elite germplasm pools, causing poor cultivar adaption to an increasing frequency of extreme climatic fluctuations.Increasing genetic variation in breeding programs is a key approach to overcome yield stagnation, but it requires efficient tools that enable breeders to characterize large populations of genotypes at a maximum resolution and low cost. Due to the high complexity of the allohexaploid wheat genome (2n = 6x = 42 chromosomes, genomic code AABBDD), which arose from three independent allopolyploidization events, deep genome analysis is notoriously difficult. Rapid genotyping platforms that can simultaneously acquire millions of genomic data points per genotype are today available for all important crop plants. These can be used to obtain population genetic parameters for the analysis of prevalent population stratification, genetic diversity or linkage disequilibrium (LD). This information is highly valuable for breeders, in order to optimize parental combinations for the creation of segregation populations with maximal genetic diversity, and to support marker-based targeted introgression of candidate genes into elite varieties, by crossing lines with high yield potentials and exotic lines that carry favorable novel alleles.In this context, this thesis describes the detailed population genetic characterization of a diverse international population of 460 wheat lines, representing global diversity from China, Europe, The United States and Australia, using the 90K single-nucleotide-polymorphism (SNP) Infinium genotyping platform. After identifying five major genetic subgroups that correspond to the ecogeographic origin of the lines, detailed measures of genetic diversity and LD were obtained at the subgenome and chromosome level. Finally, target regions were identified on all three subgenomes that are under very strong directional selection between the characterized gene pools. These selective sweeps harbor several candidate genes and QTL for agronomically important traits, such as yield, plant height or seed quality, and are thus ideal targets for a precise reinstatement of genetic variation using high-resolution marker information. This can help breeders to increase overall diversity as a key prerequisite for effective selection in breeding programs.The need to adapt modern wheat cultivars to the increasing frequency of extreme weather events has considerably raised attention on roots. However, knowledge on the genetic basis of below-ground plant development is very limited, yet powerful diagnostic markers for a genomics-based selection of improved root systems are strongly required. This dissertation describes the first genome-wide association study (GWAS) on root characteristics in hexaploid wheat to date, using a diverse population of almost 250 wheat lines in combination with high-resolution, genome-wide SNP array marker information. After identifying two QTL on chromosome 5B that are highly associated with root biomass, haplotype network analysis attributed the highest genetic effect to two rare Chinese QTL alleles whose positive epistatic interaction boosts overall root proliferation. Population genetic analysis revealed high levels of LD in this target region, which was also found to harbor candidate genes affecting spike development and heading date. Given the low level of allelic diversity of this candidate region, an indication of strong directional selection, the frequency and distribution of root and spike associated haplotype variants suggests an inadvertent co-selection of specific root-related variants in the course of selection for spike development. This could explain the low genetic diversity for these root QTL in European elite material. These findings provide breeders a means to reverse this unintended consequence of linkage drag and increase genetic variation for root growth, and lay a foundation for the subsequent functional characterization of candidate genes that affect root development in wheat.
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